Switch to kim-api c-bindings for SimulatorModel (63dcd999) · Commits · 郑智淋 / lammps

src/KIM/fix_store_kim.cpp

+7 −5

Original line number	Diff line number	Diff line
		@@ -56,7 +56,9 @@

		#include <cstring>
		#include "fix_store_kim.h"
		#include "KIM_SimulatorModel.hpp"
		extern "C" {
		#include "KIM_SimulatorModel.h"
		}
		#include "error.h"

		using namespace LAMMPS_NS;
		@@ -78,8 +80,8 @@ FixStoreKIM::~FixStoreKIM()
		// free associated storage

		if (simulator_model) {
		KIM::SimulatorModel sm = (KIM::SimulatorModel )simulator_model;
		KIM::SimulatorModel::Destroy(&sm);
		KIM_SimulatorModel sm = (KIM_SimulatorModel )simulator_model;
		KIM_SimulatorModel_Destroy(&sm);
		simulator_model = NULL;
		}

		@@ -116,8 +118,8 @@ void FixStoreKIM::setptr(const char name, void ptr)
		{
		if (strcmp(name,"simulator_model") == 0) {
		if (simulator_model) {
		KIM::SimulatorModel sm = (KIM::SimulatorModel )simulator_model;
		KIM::SimulatorModel::Destroy(&sm);
		KIM_SimulatorModel sm = (KIM_SimulatorModel )simulator_model;
		KIM_SimulatorModel_Destroy(&sm);
		}
		simulator_model = ptr;
		} else if (strcmp(name,"model_name") == 0) {

src/KIM/kim_init.cpp

+30 −30

Original line number	Diff line number	Diff line
		@@ -75,9 +75,6 @@
		extern "C" {
		#include "KIM_SimulatorHeaders.h"
		}
		//@@@@@ Need to switch to c-bindings when they are available.
		#include "KIM_SimulatorModel.hpp"
		//@@@@@

		using namespace LAMMPS_NS;

		@@ -214,29 +211,30 @@ void KimInit::determine_model_type_and_units(char * model_name,
		}
		}

		KIM::SimulatorModel * kim_SM;
		kim_error = KIM::SimulatorModel::Create(model_name, &kim_SM);
		KIM_SimulatorModel * kim_SM;
		kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM);
		if (kim_error)
		error->all(FLERR,"KIM model name not found");
		model_type = SM;

		int sim_fields;
		int sim_lines;
		std::string const * sim_field;
		std::string const * sim_value;
		kim_SM->GetNumberOfSimulatorFields(&sim_fields);
		kim_SM->CloseTemplateMap();
		char const * sim_field;
		char const * sim_value;
		KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields);
		KIM_SimulatorModel_CloseTemplateMap(kim_SM);
		for (int i=0; i < sim_fields; ++i) {
		kim_SM->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
		KIM_SimulatorModel_GetSimulatorFieldMetadata(
		kim_SM,i,&sim_lines,&sim_field);

		if (*sim_field == "units") {
		kim_SM->GetSimulatorFieldLine(i,0,&sim_value);
		int len=(*sim_value).length()+1;
		model_units = new char[len]; strcpy(model_units,sim_value->c_str());
		if (0 == strcmp(sim_field,"units")) {
		KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value);
		int len=strlen(sim_value)+1;
		model_units = new char[len]; strcpy(model_units,sim_value);
		break;
		}
		}
		KIM::SimulatorModel::Destroy(&kim_SM);
		KIM_SimulatorModel_Destroy(&kim_SM);

		if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) {
		std::string mesg("Incompatible units for KIM Simulator Model, "
		@@ -271,16 +269,16 @@ void KimInit::do_init(char model_name, char user_units, char *model_units)
		kim_init_log_delimiter("begin");

		int kimerror;
		// @@@@@ switch to c-bindings when they are available
		KIM::SimulatorModel * simulatorModel;
		KIM_SimulatorModel * simulatorModel;
		if (model_type == SM)
		{
		kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel);
		kimerror = KIM_SimulatorModel_Create(model_name,&simulatorModel);

		const std::string sim_name, sim_version;
		simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version);
		char const sim_name, sim_version;
		KIM_SimulatorModel_GetSimulatorNameAndVersion(
		simulatorModel,&sim_name, &sim_version);

		if (*sim_name != "LAMMPS")
		if (0 != strcmp(sim_name,"LAMMPS"))
		error->all(FLERR,"Incompatible KIM Simulator Model");

		if (comm->me == 0) {
		@@ -288,7 +286,7 @@ void KimInit::do_init(char model_name, char user_units, char *model_units)
		mesg += model_name;
		mesg += "\n";
		mesg += "# For Simulator : ";
		mesg += sim_name + " " + sim_version + "\n";
		mesg += std::string(sim_name) + " " + sim_version + "\n";
		mesg += "# Running on : LAMMPS ";
		mesg += universe->version;
		mesg += "\n";
		@@ -302,7 +300,7 @@ void KimInit::do_init(char model_name, char user_units, char *model_units)

		// need to call this to have access to (some) simulator model init data.

		simulatorModel->CloseTemplateMap();
		KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
		}

		// Define unit conversion factor variables and print to log
		@@ -316,24 +314,26 @@ void KimInit::do_init(char model_name, char user_units, char *model_units)

		if (model_type == SM) {
		int sim_fields, sim_lines;
		const std::string sim_field, sim_value;
		simulatorModel->GetNumberOfSimulatorFields(&sim_fields);
		char const sim_field, sim_value;
		KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);

		// init model

		for (int i=0; i < sim_fields; ++i) {
		simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
		if (*sim_field == "model-init") {
		KIM_SimulatorModel_GetSimulatorFieldMetadata(
		simulatorModel,i,&sim_lines,&sim_field);
		if (0 == strcmp(sim_field,"model-init")) {
		for (int j=0; j < sim_lines; ++j) {
		simulatorModel->GetSimulatorFieldLine(i,j,&sim_value);
		input->one(sim_value->c_str());
		KIM_SimulatorModel_GetSimulatorFieldLine(
		simulatorModel,i,j,&sim_value);
		input->one(sim_value);
		}
		break;
		}
		}

		// reset template map.
		simulatorModel->OpenAndInitializeTemplateMap();
		KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel);
		}

		// End output to log file

src/KIM/kim_interactions.cpp

+26 −23

Original line number	Diff line number	Diff line
		@@ -73,9 +73,6 @@
		extern "C" {
		#include "KIM_SimulatorHeaders.h"
		}
		//@@@@@ Need to switch to c-bindings when they are available.
		#include "KIM_SimulatorModel.hpp"
		//@@@@@

		#define SNUM(x) \
		static_cast<std::ostringstream const &>(std::ostringstream() \
		@@ -122,7 +119,7 @@ void KimInteractions::do_setup(int narg, char **arg)
		error->all(FLERR,"Illegal kim_interactions command");

		char *model_name = NULL;
		KIM::SimulatorModel *simulatorModel(NULL);
		KIM_SimulatorModel *simulatorModel(NULL);

		// check if we had a kim_init command by finding fix STORE/KIM
		// retrieve model name and pointer to simulator model class instance.
		@@ -132,7 +129,7 @@ void KimInteractions::do_setup(int narg, char **arg)
		if (ifix >= 0) {
		FixStoreKIM fix_store = (FixStoreKIM ) modify->fix[ifix];
		model_name = (char *)fix_store->getptr("model_name");
		simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model");
		simulatorModel = (KIM_SimulatorModel *)fix_store->getptr("simulator_model");
		} else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'");

		// Begin output to log file
		@@ -151,9 +148,11 @@ void KimInteractions::do_setup(int narg, char **arg)
		delimiter = " ";
		}

		simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list);
		simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list);
		simulatorModel->CloseTemplateMap();
		KIM_SimulatorModel_AddTemplateMap(
		simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str());
		KIM_SimulatorModel_AddTemplateMap(
		simulatorModel,"atom-type-num-list",atom_type_num_list.c_str());
		KIM_SimulatorModel_CloseTemplateMap(simulatorModel);

		int len = strlen(atom_type_sym_list.c_str())+1;
		char *strbuf = new char[len];
		@@ -163,16 +162,17 @@ void KimInteractions::do_setup(int narg, char **arg)

		int sim_num_species;
		bool species_is_supported;
		const std::string *sim_species;
		simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species);
		char const *sim_species;
		KIM_SimulatorModel_GetNumberOfSupportedSpecies(
		simulatorModel,&sim_num_species);
		strcpy(strbuf,atom_type_sym_list.c_str());
		strword = strtok(strbuf," \t");
		while (strword) {
		species_is_supported = false;
		if (strcmp(strword,"NULL") == 0) continue;
		for (int i=0; i < sim_num_species; ++i) {
		simulatorModel->GetSupportedSpecies(i, &sim_species);
		if (strcmp(sim_species->c_str(),strword) == 0)
		KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species);
		if (strcmp(sim_species,strword) == 0)
		species_is_supported = true;
		}
		if (!species_is_supported) {
		@@ -188,26 +188,29 @@ void KimInteractions::do_setup(int narg, char **arg)
		// check if units are unchanged

		int sim_fields, sim_lines;
		const std::string sim_field, sim_value;
		simulatorModel->GetNumberOfSimulatorFields(&sim_fields);
		const char sim_field, sim_value;
		KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
		for (int i=0; i < sim_fields; ++i) {
		simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
		KIM_SimulatorModel_GetSimulatorFieldMetadata(
		simulatorModel,i,&sim_lines,&sim_field);

		if (*sim_field == "units") {
		simulatorModel->GetSimulatorFieldLine(i,0,&sim_value);
		if (*sim_value != update->unit_style)
		if (0 == strcmp(sim_field,"units")) {
		KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel,i,0,&sim_value);
		if (0 != strcmp(sim_value,update->unit_style))
		error->all(FLERR,"Incompatible units for KIM Simulator Model");
		}
		}

		int sim_model_idx=-1;
		for (int i=0; i < sim_fields; ++i) {
		simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
		if (*sim_field == "model-defn") {
		KIM_SimulatorModel_GetSimulatorFieldMetadata(
		simulatorModel,i,&sim_lines,&sim_field);
		if (0 == strcmp(sim_field,"model-defn")) {
		sim_model_idx = i;
		for (int j=0; j < sim_lines; ++j) {
		simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value);
		input->one(sim_value->c_str());
		KIM_SimulatorModel_GetSimulatorFieldLine(
		simulatorModel,sim_model_idx,j,&sim_value);
		input->one(sim_value);
		}
		}
		}
		@@ -215,7 +218,7 @@ void KimInteractions::do_setup(int narg, char **arg)
		if (sim_model_idx < 0)
		error->all(FLERR,"KIM Simulator Model has no Model definition");

		simulatorModel->OpenAndInitializeTemplateMap();
		KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel);

		} else {

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